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I have a template file (namely /lib/systemd/system/systemd-nspawn@.service) which has an ExecStart entry.

This entry is correct for all services started from that template, except for one. For that special one (say systemd-nspawn@specialcontainer.service) I would like to have a different ExecStart.

For non-template services, I would in that case use a drop-in. Is there an equivalent for template-based service units? I would need a way to inform systemd that this is "a drop-in for the template service unit, when %i is specialcontainer"

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Yep - this is possible.

You need to have an override .d folder for the exact service name you want to override - you can see this quite nicely if you do

sudo systemctl edit systemd-nspawn@specialcontainer.service

This will create a file (on my machine at least, running Ubuntu 16.04) at /etc/systemd/system/systemd-nspawn@specialcontainer.service.d/override.conf with changes.

https://askubuntu.com/a/659268/915810 has a way more comprehensive answer - using the getty template systemd unit as an example.

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